Mutations in iron-sulfur cluster proteins that improve xylose utilization

Abstract

There is provided an engineered host cells comprising (a) one or more mutations in one or more endogenous genes encoding a protein associated with iron metabolism; and (b) at least one gene encoding a polypeptide having xylose isomerase activity, and methods of their use thereof.

The invention claimed is: 
     
       1. A recombinant yeast cell comprising (a) at least one heterologous gene encoding a protein associated with iron metabolism; and (b) at least one heterologous gene encoding a polypeptide having xylose isomerase activity, wherein the heterologous gene (b) encodes a polypeptide having at least 80%, 85%, 90%, 95% or 100% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 35, 37, 39 and 41. 
     
     
       2. The recombinant yeast cell of  claim 1 , wherein the heterologous gene (a) is selected from the group consisting of AFT1, AFT2, and orthologues and combinations thereof. 
     
     
       3. The recombinant yeast cell of  claim 1 , wherein heterologous gene (a) encodes a protein that increases the activity of Aft1 and/or Aft2 and/or increases the expression of AFT1 and/or AFT2 and/or suppresses or inhibits the activity and/or expression of a protein that suppresses or inhibits the activity of Aft1 and/or Aft2 and/or suppresses or inhibits the expression of AFT1 and/or AFT2. 
     
     
       4. The recombinant yeast cell of  claim 1 , wherein the heterologous gene encodes a target of Aft1 and/or Aft2. 
     
     
       5. The recombinant yeast cell of  claim 1 , wherein the heterologous gene (a) encodes a polypeptide having iron transport activity. 
     
     
       6. The recombinant yeast cell of  claim 1 , the recombinant yeast cell further comprises one or more mutations in one or more endogenous genes encoding a protein associated with iron metabolism. 
     
     
       7. The recombinant yeast cell of  claim 6 , wherein the one or more mutations in one ore more endogenous genes is in a gene of ISU1, YFH1, NFS1, AFT1, AFT2, YAP5, FRA1, FRA2, GREX3, GREX4, CCC1, or any combination thereof. 
     
     
       8. The recombinant yeast cell of  claim 6 , wherein the recombinant yeast cell comprises one or more mutations in the endogenous ISU1 gene that results in a polypeptide comprising at least one amino acid substitution selected from the group consisting of D71N, D71G, and S98F, wherein the position of the substitution is relative to the amino acid positions of SEQ ID NO:29. 
     
     
       9. The recombinant yeast cell of  claim 6 , wherein the recombinant yeast cell comprises one or more mutations in the endogenous YFH1 gene that results in a polypeptide comprising a T163P substitution, wherein the position of the substitution is relative to the amino acid positions of SEQ ID NO:31. 
     
     
       10. The recombinant yeast cell of  claim 6 , wherein the recombinant yeast cell comprises one or more mutations in the endogenous NFS1 gene that results in a polypeptide comprising at least one amino acid substitution selected from the group consisting of L115W and E458D, wherein the position of the substitution is relative to the amino acid positions of SEQ ID NO:33. 
     
     
       11. The recombinant yeast cell of  claim 6 , wherein the recombinant yeast cell comprises a mutation in the endogenous AFT1 gene that results in increased Aft1 activity and/or a mutation in the endogenous AFT2 gene that results in increased Aft2 activity. 
     
     
       12. The recombinant yeast cell of  claim 6 , wherein the recombinant yeast cell comprises one or more mutations in one or more endogenous genes FRA1, FRA2, GREX3, or GREX4; wherein the one or more mutations results in increased activity of Aft1 and/or Aft2; and/or wherein the one or more mutations results in increased expression of one or more genes regulated by Aft1 and/or Aft2. 
     
     
       13. The recombinant yeast cell of  claim 6 , wherein the recombinant yeast cell further comprises a mutation in an endogenous gene selected from the group consisting of YAP5 and CCC1. 
     
     
       14. The recombinant yeast cell of  claim 1 , wherein the recombinant yeast cell further comprises at least one genetic modification of one or more endogenous genes encoding a protein of the pentose phosphate pathway. 
     
     
       15. The recombinant yeast cell of  claim 14 , wherein the recombinant, yeast cell comprises at least one genetic modification in at least one of the endogenous genes selectec the group consisting of XKS1, RKI1, RPE1, TKL1, and TAL1. 
     
     
       16. The recombinant yeast cell of  claim 1 , wherein the recombinant yeast cell further comprises a deletion or disruption of one or more aldose reductase genes. 
     
     
       17. The recombinant yeast cell of  claim 16 , wherein the aldose reductase gene is GRE3 or YPR1. 
     
     
       18. The recombinant yeast cell of any one of  claim 17 , wherein the yeast cell further comprises a modification of the endogenous PGM1 gene. 
     
     
       19. The recombinant yeast cell of  claim 1 , wherein the recombinant yeast cell comprises heterologous expression of one or more polynucleotides encoding XKS1, RKI1, RPE1, TKL1, and/or TAL1. 
     
     
       20. The recombinant yeast cell of  claim 1 , wherein the heterologous gene (b) encodes a polypeptide having at least 80% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, and 27. 
     
     
       21. A method for producing a fermentation product comprising contacting the recombinant yeast cell of  claim 1  with a carbon source, wherein said carbon source comprises xylose and/or xylan.